## 342 samples selected for analysis
## 395 files found
## The following files do not have a matching metadata entry:
## [1] "AA05141" "AA05181" "X500006_2" "X500016_2" "X500017_2" "X500082_2" "X500110_2" "X500126_2" "X500161_2" "X500224_2" "X500471_2" "X500500_2" "X500519_2" "X500523_2" "X500531_2" "X500533_2" "X500534_2" "X500535_2" "X510008_2" "X510010_2" "X533070_2" "X533071_2" "X533181_2" "X533182_2" "X541038_2" "X541183_2" "X541728_2" "X541980_2" "X550004_2" "X590013_2" "X590015_2" "X590048_2" "X590098_2" "X590113_2" "X500133_2" "X500544_2" "X500545_2" "X500576_2" "X500584_2" "X500586_2" "X500587_2" "X500588_2" "X500589_2" "X500590_2" "X510033_2" "X541051_2" "X541052_2" "X541091_2" "X541191_2" "X598101_2" "S00727_V07059_2" "S01248_V07399_2" "AA04447"
## All expected files found.
Samples with a PC1 > 2 (the red lines) and/or PC2 zscore > 2.5 (the green lines) were dropped from analysis. Points in red represent samples that were dropped.
| sample_name | visit_ref | subject_ref | sex | ethnicity | age |
|---|---|---|---|---|---|
| AA05198 | PCV|500802|2020-10-20 | PCV|500802 | Female | [AI] | 43 |
| AA05201 | PCV|500808|2020-10-29 | PCV|500808 | Female | [EA] | 77 |
| AA05222 | PCV|500810|2020-12-09 | PCV|500810 | Female | [AI] | NA |
| AA05081 | ORDRCC|500643|2019-08-12 | ORDRCC|500643 | Female | [AI] | NA |
| AA05197 | ORDRCC|541174|2020-11-11 | ORDRCC|541174 | Female | [EA] | NA |
| X541052 | ORDRCC|541052|2019-01-24 | ORDRCC|541052 | Female | [EA] | 66 |
| AA02818 | MDFL|541038|2017-04-20 | MDFL|541038 | Female | [EA] | 32 |
| AA02821 | MDFL|500531|2017-06-27 | MDFL|500531 | Female | [AA] | 60 |
| AA02817 | MDFL|500519|2017-04-20 | MDFL|500519 | Female | [EA] | 33 |
| AA02819 | MDFL|500006|2017-05-01 | MDFL|500006 | Female | [AA] | 42 |
This MA plot is of shrunken log2 fold changes (using the apeglm package), in which actual fold changes are adjusted to compensate for the high variablity of genes with few counts.
Dots in red indicate a significant expression difference between Control and SLE.
Surrogate variables are unknown, unmodeled, or latent sources of noise hidden in the data. The sva package was used to estimate the first three surrogate variables which were then introduced into the DESeq design formula to control for their effects.
To determine the optimal k, the gap statistic was calculated for k = (3,20) (k = 2 was ignored because it just returns the two disease clusters). A higher coefficient means better intracluster simliarity and intercluster differences.
To determine if there is a gross mixup of samples, examine the expression of sex-specific transcripts to ensure that only female-subject samples express “XIST” and male-subject samples "DDX3Y:
There appears to be one sample that is lacking a label but appears to express high levels of the female markers XIST and ZFX as well as the male markers PCDH11Y and PRORY. There’s also a couple of other samples that may have a mix of male and female markers, but otherwise no signs of gross sample mixup.
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.0.4 (2021-02-15)
## os Ubuntu 20.04 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Etc/UTC
## date 2021-03-19
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date lib source
## abind 1.4-5 2016-07-21 [1] RSPM (R 4.0.4)
## annotate 1.68.0 2020-10-27 [1] Bioconductor
## AnnotationDbi 1.52.0 2020-10-27 [1] RSPM (R 4.0.4)
## apeglm 1.12.0 2020-10-27 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.0.3)
## backports 1.2.1 2020-12-09 [1] RSPM (R 4.0.4)
## base64enc 0.1-3 2015-07-28 [1] RSPM (R 4.0.3)
## base64url 1.4 2018-05-14 [1] RSPM (R 4.0.4)
## bbmle 1.0.23.1 2020-02-03 [1] RSPM (R 4.0.3)
## bdsmatrix 1.3-4 2020-01-13 [1] RSPM (R 4.0.3)
## Biobase * 2.50.0 2020-10-27 [1] RSPM (R 4.0.4)
## BiocGenerics * 0.36.0 2020-10-27 [1] RSPM (R 4.0.4)
## BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.4)
## BiocParallel * 1.24.1 2020-11-06 [1] RSPM (R 4.0.4)
## bit 4.0.4 2020-08-04 [1] RSPM (R 4.0.3)
## bit64 4.0.5 2020-08-30 [1] RSPM (R 4.0.3)
## bitops 1.0-6 2013-08-17 [1] RSPM (R 4.0.4)
## blob 1.2.1 2020-01-20 [1] RSPM (R 4.0.4)
## broom * 0.7.5 2021-02-19 [1] RSPM (R 4.0.4)
## bslib 0.2.4 2021-01-25 [1] RSPM (R 4.0.4)
## cachem 1.0.4 2021-02-13 [1] RSPM (R 4.0.3)
## car 3.0-10 2020-09-29 [1] RSPM (R 4.0.4)
## carData 3.0-4 2020-05-22 [1] RSPM (R 4.0.4)
## caret * 6.0-86 2020-03-20 [1] RSPM (R 4.0.3)
## cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.0.4)
## checkmate 2.0.0 2020-02-06 [1] RSPM (R 4.0.4)
## class 7.3-18 2021-01-24 [2] CRAN (R 4.0.4)
## cli 2.3.1 2021-02-23 [1] RSPM (R 4.0.3)
## cluster * 2.1.1 2021-02-14 [1] RSPM (R 4.0.3)
## clusterProfiler * 3.18.1 2021-02-09 [1] Bioconductor
## coda 0.19-4 2020-09-30 [1] RSPM (R 4.0.3)
## codetools 0.2-18 2020-11-04 [2] CRAN (R 4.0.4)
## colorspace 2.0-0 2020-11-11 [1] RSPM (R 4.0.4)
## corrplot * 0.84 2017-10-16 [1] RSPM (R 4.0.4)
## cowplot * 1.1.1 2020-12-30 [1] RSPM (R 4.0.4)
## crayon 1.4.1 2021-02-08 [1] RSPM (R 4.0.3)
## crosstalk 1.1.1 2021-01-12 [1] RSPM (R 4.0.3)
## curl 4.3 2019-12-02 [1] RSPM (R 4.0.3)
## data.table * 1.14.0 2021-02-21 [1] RSPM (R 4.0.4)
## DBI 1.1.1 2021-01-15 [1] RSPM (R 4.0.4)
## dbplyr 2.1.0 2021-02-03 [1] RSPM (R 4.0.4)
## DelayedArray 0.16.2 2021-02-26 [1] RSPM (R 4.0.4)
## DESeq2 * 1.30.1 2021-02-19 [1] RSPM (R 4.0.4)
## dials * 0.0.9 2020-09-16 [1] RSPM (R 4.0.3)
## DiceDesign 1.9 2021-02-13 [1] RSPM (R 4.0.3)
## digest 0.6.27 2020-10-24 [1] RSPM (R 4.0.3)
## DO.db 2.9 2021-03-13 [1] RSPM (R 4.0.4)
## doParallel 1.0.16 2020-10-16 [1] RSPM (R 4.0.4)
## DOSE 3.16.0 2020-10-27 [1] RSPM (R 4.0.4)
## downloader 0.4 2015-07-09 [1] RSPM (R 4.0.4)
## dplyr * 1.0.5 2021-03-05 [1] RSPM (R 4.0.4)
## drake * 7.13.1 2021-02-03 [1] RSPM (R 4.0.4)
## dynamicTreeCut * 1.63-1 2016-03-11 [1] RSPM (R 4.0.4)
## edgeR 3.32.1 2021-01-14 [1] RSPM (R 4.0.4)
## ellipsis 0.3.1 2020-05-15 [1] RSPM (R 4.0.3)
## emdbook 1.3.12 2020-02-19 [1] RSPM (R 4.0.0)
## enrichplot 1.10.2 2021-01-28 [1] RSPM (R 4.0.4)
## evaluate 0.14 2019-05-28 [1] RSPM (R 4.0.3)
## factoextra * 1.0.7 2020-04-01 [1] RSPM (R 4.0.3)
## fansi 0.4.2 2021-01-15 [1] RSPM (R 4.0.3)
## farver 2.1.0 2021-02-28 [1] RSPM (R 4.0.4)
## fastcluster * 1.1.25 2018-06-07 [1] RSPM (R 4.0.4)
## fastmap 1.1.0 2021-01-25 [1] RSPM (R 4.0.3)
## fastmatch 1.1-0 2017-01-28 [1] RSPM (R 4.0.4)
## fgsea 1.16.0 2020-10-27 [1] RSPM (R 4.0.4)
## filelock 1.0.2 2018-10-05 [1] RSPM (R 4.0.4)
## flextable * 0.6.4 2021-03-10 [1] RSPM (R 4.0.3)
## FNN 1.1.3 2019-02-15 [1] RSPM (R 4.0.4)
## forcats * 0.5.1 2021-01-27 [1] RSPM (R 4.0.4)
## foreach 1.5.1 2020-10-15 [1] RSPM (R 4.0.4)
## foreign 0.8-81 2020-12-22 [2] CRAN (R 4.0.4)
## formattable * 0.2.1 2021-01-07 [1] RSPM (R 4.0.4)
## Formula 1.2-4 2020-10-16 [1] RSPM (R 4.0.4)
## fs 1.5.0 2020-07-31 [1] RSPM (R 4.0.3)
## furrr * 0.2.2 2021-01-29 [1] RSPM (R 4.0.4)
## future * 1.21.0 2020-12-10 [1] RSPM (R 4.0.4)
## gdtools 0.2.3 2021-01-06 [1] RSPM (R 4.0.3)
## genefilter * 1.72.1 2021-01-21 [1] RSPM (R 4.0.4)
## geneplotter 1.68.0 2020-10-27 [1] RSPM (R 4.0.4)
## generics 0.1.0 2020-10-31 [1] RSPM (R 4.0.4)
## GenomeInfoDb * 1.26.4 2021-03-10 [1] Bioconductor
## GenomeInfoDbData 1.2.4 2021-03-13 [1] RSPM (R 4.0.4)
## GenomicRanges * 1.42.0 2020-10-27 [1] RSPM (R 4.0.4)
## ggfittext 0.9.1 2021-01-30 [1] RSPM (R 4.0.4)
## ggforce * 0.3.3 2021-03-05 [1] RSPM (R 4.0.4)
## ggplot2 * 3.3.3 2020-12-30 [1] RSPM (R 4.0.4)
## ggplotify * 0.0.5 2020-03-12 [1] RSPM (R 4.0.0)
## ggpubr * 0.4.0 2020-06-27 [1] RSPM (R 4.0.4)
## ggradar * 0.2 2021-03-16 [1] Github (ricardo-bion/ggradar@63e5cef)
## ggraph 2.0.5 2021-02-23 [1] RSPM (R 4.0.4)
## ggrepel * 0.9.1 2021-01-15 [1] RSPM (R 4.0.3)
## ggsignif 0.6.1 2021-02-23 [1] RSPM (R 4.0.4)
## ggtext * 0.1.1 2020-12-17 [1] RSPM (R 4.0.3)
## globals 0.14.0 2020-11-22 [1] RSPM (R 4.0.4)
## glue 1.4.2 2020-08-27 [1] RSPM (R 4.0.3)
## GO.db 3.12.1 2021-03-13 [1] RSPM (R 4.0.4)
## GOSemSim 2.16.1 2020-10-29 [1] RSPM (R 4.0.4)
## gower 0.2.2 2020-06-23 [1] RSPM (R 4.0.3)
## GPfit 1.0-8 2019-02-08 [1] RSPM (R 4.0.3)
## graphlayouts 0.7.1 2020-10-26 [1] RSPM (R 4.0.4)
## gridBase 0.4-7 2014-02-24 [1] RSPM (R 4.0.4)
## gridExtra 2.3 2017-09-09 [1] RSPM (R 4.0.4)
## gridGraphics 0.5-1 2020-12-13 [1] RSPM (R 4.0.3)
## gridtext 0.1.4 2020-12-10 [1] RSPM (R 4.0.4)
## gtable 0.3.0 2019-03-25 [1] RSPM (R 4.0.4)
## gtools * 3.8.2 2020-03-31 [1] RSPM (R 4.0.4)
## haven 2.3.1 2020-06-01 [1] RSPM (R 4.0.4)
## here * 1.0.1 2020-12-13 [1] RSPM (R 4.0.4)
## HGNChelper * 0.8.1 2019-10-24 [1] RSPM (R 4.0.0)
## highr 0.8 2019-03-20 [1] RSPM (R 4.0.3)
## Hmisc 4.5-0 2021-02-28 [1] RSPM (R 4.0.4)
## hms 1.0.0 2021-01-13 [1] RSPM (R 4.0.4)
## htmlTable 2.1.0 2020-09-16 [1] RSPM (R 4.0.4)
## htmltools 0.5.1.1 2021-01-22 [1] RSPM (R 4.0.3)
## htmlwidgets 1.5.3 2020-12-10 [1] RSPM (R 4.0.3)
## httr 1.4.2 2020-07-20 [1] RSPM (R 4.0.3)
## igraph 1.2.6 2020-10-06 [1] RSPM (R 4.0.4)
## impute 1.64.0 2020-10-27 [1] RSPM (R 4.0.4)
## infer * 0.5.4 2021-01-13 [1] RSPM (R 4.0.3)
## inspectdf * 0.0.10 2021-02-20 [1] RSPM (R 4.0.4)
## ipred 0.9-11 2021-03-12 [1] RSPM (R 4.0.3)
## IRanges * 2.24.1 2020-12-12 [1] RSPM (R 4.0.4)
## irlba * 2.3.3 2019-02-05 [1] RSPM (R 4.0.3)
## iterators 1.0.13 2020-10-15 [1] RSPM (R 4.0.4)
## janitor * 2.1.0 2021-01-05 [1] RSPM (R 4.0.4)
## jpeg 0.1-8.1 2019-10-24 [1] RSPM (R 4.0.4)
## jquerylib 0.1.3 2020-12-17 [1] RSPM (R 4.0.4)
## jsonlite 1.7.2 2020-12-09 [1] RSPM (R 4.0.3)
## kableExtra * 1.3.4 2021-02-20 [1] RSPM (R 4.0.4)
## knitr * 1.31 2021-01-27 [1] RSPM (R 4.0.3)
## labeling 0.4.2 2020-10-20 [1] RSPM (R 4.0.4)
## lattice * 0.20-41 2020-04-02 [2] CRAN (R 4.0.4)
## latticeExtra 0.6-29 2019-12-19 [1] RSPM (R 4.0.4)
## lava 1.6.9 2021-03-11 [1] RSPM (R 4.0.3)
## lazyeval 0.2.2 2019-03-15 [1] RSPM (R 4.0.3)
## lhs 1.1.1 2020-10-05 [1] RSPM (R 4.0.3)
## lifecycle 1.0.0 2021-02-15 [1] RSPM (R 4.0.3)
## limma 3.46.0 2020-10-27 [1] RSPM (R 4.0.4)
## listenv 0.8.0 2019-12-05 [1] RSPM (R 4.0.4)
## locfit 1.5-9.4 2020-03-25 [1] RSPM (R 4.0.4)
## lubridate 1.7.10 2021-02-26 [1] RSPM (R 4.0.4)
## magrittr * 2.0.1 2020-11-17 [1] RSPM (R 4.0.3)
## MASS 7.3-53.1 2021-02-12 [2] RSPM (R 4.0.3)
## Matrix * 1.3-2 2021-01-06 [2] CRAN (R 4.0.4)
## MatrixGenerics * 1.2.1 2021-01-30 [1] RSPM (R 4.0.4)
## matrixStats * 0.58.0 2021-01-29 [1] RSPM (R 4.0.4)
## memoise 2.0.0 2021-01-26 [1] RSPM (R 4.0.3)
## mgcv * 1.8-34 2021-02-16 [2] RSPM (R 4.0.3)
## modeldata * 0.1.0 2020-10-22 [1] RSPM (R 4.0.3)
## ModelMetrics 1.2.2.2 2020-03-17 [1] RSPM (R 4.0.3)
## modelr 0.1.8 2020-05-19 [1] RSPM (R 4.0.4)
## moduleScoreR * 0.0.0.9200 2021-03-13 [1] Github (milescsmith/moduleScoreR@e6db70f)
## munsell 0.5.0 2018-06-12 [1] RSPM (R 4.0.4)
## mvtnorm 1.1-1 2020-06-09 [1] RSPM (R 4.0.3)
## nlme * 3.1-152 2021-02-04 [2] CRAN (R 4.0.4)
## NMF 0.23.0 2020-08-01 [1] RSPM (R 4.0.4)
## nnet 7.3-15 2021-01-24 [2] CRAN (R 4.0.4)
## numDeriv 2016.8-1.1 2019-06-06 [1] RSPM (R 4.0.4)
## oaColors * 0.0.4 2015-11-30 [1] RSPM (R 4.0.0)
## officer 0.3.17 2021-03-05 [1] RSPM (R 4.0.3)
## openxlsx 4.2.3 2020-10-27 [1] RSPM (R 4.0.4)
## paletteer * 1.3.0 2021-01-06 [1] RSPM (R 4.0.4)
## parallelDist 0.2.4 2018-12-12 [1] RSPM (R 4.0.4)
## parallelly 1.24.0 2021-03-14 [1] RSPM (R 4.0.3)
## parsnip * 0.1.5 2021-01-19 [1] RSPM (R 4.0.3)
## pheatmap * 1.0.12 2019-01-04 [1] RSPM (R 4.0.4)
## pillar 1.5.1 2021-03-05 [1] RSPM (R 4.0.3)
## pkgconfig 2.0.3 2019-09-22 [1] RSPM (R 4.0.3)
## pkgmaker 0.32.2 2020-10-20 [1] RSPM (R 4.0.4)
## plotly * 4.9.3 2021-01-10 [1] RSPM (R 4.0.4)
## plyr 1.8.6 2020-03-03 [1] RSPM (R 4.0.4)
## png 0.1-7 2013-12-03 [1] RSPM (R 4.0.4)
## polyclip 1.10-0 2019-03-14 [1] RSPM (R 4.0.4)
## preprocessCore 1.52.1 2021-01-08 [1] RSPM (R 4.0.4)
## prettyunits 1.1.1 2020-01-24 [1] RSPM (R 4.0.3)
## pROC 1.17.0.1 2021-01-13 [1] RSPM (R 4.0.3)
## prodlim 2019.11.13 2019-11-17 [1] RSPM (R 4.0.3)
## progress 1.2.2 2019-05-16 [1] RSPM (R 4.0.4)
## purrr * 0.3.4 2020-04-17 [1] RSPM (R 4.0.3)
## qvalue 2.22.0 2020-10-27 [1] RSPM (R 4.0.4)
## R6 2.5.0 2020-10-28 [1] RSPM (R 4.0.3)
## randomForest * 4.6-14 2018-03-25 [1] RSPM (R 4.0.3)
## RColorBrewer * 1.1-2 2014-12-07 [1] RSPM (R 4.0.3)
## Rcpp 1.0.6 2021-01-15 [1] RSPM (R 4.0.4)
## RcppParallel 5.0.3 2021-02-24 [1] RSPM (R 4.0.4)
## RCurl 1.98-1.2 2020-04-18 [1] RSPM (R 4.0.4)
## readr * 1.4.0 2020-10-05 [1] RSPM (R 4.0.4)
## readxl * 1.3.1 2019-03-13 [1] RSPM (R 4.0.3)
## recipes * 0.1.15 2020-11-11 [1] RSPM (R 4.0.3)
## registry 0.5-1 2019-03-05 [1] RSPM (R 4.0.4)
## rematch2 2.1.2 2020-05-01 [1] RSPM (R 4.0.3)
## reprex 1.0.0 2021-01-27 [1] RSPM (R 4.0.4)
## reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.0.4)
## reticulate 1.18 2020-10-25 [1] RSPM (R 4.0.4)
## rio 0.5.26 2021-03-01 [1] RSPM (R 4.0.4)
## rlang * 0.4.10 2020-12-30 [1] RSPM (R 4.0.3)
## rmarkdown * 2.7 2021-02-19 [1] RSPM (R 4.0.4)
## rngtools 1.5 2020-01-23 [1] RSPM (R 4.0.4)
## rpart 4.1-15 2019-04-12 [2] CRAN (R 4.0.4)
## rprojroot 2.0.2 2020-11-15 [1] RSPM (R 4.0.3)
## rsample * 0.0.9 2021-02-17 [1] RSPM (R 4.0.3)
## RSpectra 0.16-0 2019-12-01 [1] RSPM (R 4.0.4)
## RSQLite 2.2.4 2021-03-12 [1] RSPM (R 4.0.3)
## rstatix * 0.7.0 2021-02-13 [1] RSPM (R 4.0.4)
## rstudioapi 0.13 2020-11-12 [1] RSPM (R 4.0.3)
## rsvd 1.0.3 2020-02-17 [1] RSPM (R 4.0.4)
## rvcheck 0.1.8 2020-03-01 [1] RSPM (R 4.0.4)
## rvest 1.0.0 2021-03-09 [1] RSPM (R 4.0.4)
## S4Vectors * 0.28.1 2020-12-09 [1] RSPM (R 4.0.4)
## sass 0.3.1 2021-01-24 [1] RSPM (R 4.0.4)
## scales * 1.1.1 2020-05-11 [1] RSPM (R 4.0.3)
## scatterpie 0.1.5 2020-09-09 [1] RSPM (R 4.0.4)
## sessioninfo 1.1.1 2018-11-05 [1] RSPM (R 4.0.3)
## shadowtext 0.0.7 2019-11-06 [1] RSPM (R 4.0.4)
## snakecase 0.11.0 2019-05-25 [1] RSPM (R 4.0.4)
## snow 0.4-3 2018-09-14 [1] RSPM (R 4.0.4)
## storr 1.2.5 2020-12-01 [1] RSPM (R 4.0.4)
## stringi 1.5.3 2020-09-09 [1] RSPM (R 4.0.3)
## stringr * 1.4.0 2019-02-10 [1] RSPM (R 4.0.3)
## SummarizedExperiment * 1.20.0 2020-10-27 [1] RSPM (R 4.0.4)
## survival 3.2-7 2020-09-28 [2] CRAN (R 4.0.4)
## sva * 3.38.0 2020-10-27 [1] Bioconductor
## svglite 2.0.0 2021-02-20 [1] RSPM (R 4.0.4)
## systemfonts 1.0.1 2021-02-09 [1] RSPM (R 4.0.4)
## tibble * 3.1.0 2021-02-25 [1] RSPM (R 4.0.3)
## tidygraph 1.2.0 2020-05-12 [1] RSPM (R 4.0.4)
## tidymodels * 0.1.2 2020-11-22 [1] RSPM (R 4.0.3)
## tidyr * 1.1.3 2021-03-03 [1] RSPM (R 4.0.4)
## tidyselect 1.1.0 2020-05-11 [1] RSPM (R 4.0.4)
## tidyverse * 1.3.0 2019-11-21 [1] RSPM (R 4.0.4)
## timeDate 3043.102 2018-02-21 [1] RSPM (R 4.0.3)
## tune * 0.1.3 2021-02-28 [1] RSPM (R 4.0.3)
## tweenr 1.0.1 2018-12-14 [1] RSPM (R 4.0.4)
## tximport * 1.18.0 2020-10-27 [1] RSPM (R 4.0.4)
## txtq 0.2.3 2020-06-23 [1] RSPM (R 4.0.4)
## utf8 1.2.1 2021-03-12 [1] RSPM (R 4.0.3)
## uuid 0.1-4 2020-02-26 [1] RSPM (R 4.0.3)
## uwot * 0.1.10 2020-12-15 [1] RSPM (R 4.0.4)
## vctrs 0.3.6 2020-12-17 [1] RSPM (R 4.0.3)
## viridis * 0.5.1 2018-03-29 [1] RSPM (R 4.0.3)
## viridisLite * 0.3.0 2018-02-01 [1] RSPM (R 4.0.4)
## webshot 0.5.2 2019-11-22 [1] RSPM (R 4.0.4)
## WGCNA * 1.70-3 2021-02-28 [1] RSPM (R 4.0.4)
## withr 2.4.1 2021-01-26 [1] RSPM (R 4.0.3)
## workflows * 0.2.2 2021-03-10 [1] RSPM (R 4.0.3)
## xfun 0.22 2021-03-11 [1] RSPM (R 4.0.3)
## XML 3.99-0.5 2020-07-23 [1] RSPM (R 4.0.4)
## xml2 1.3.2 2020-04-23 [1] RSPM (R 4.0.3)
## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.0.4)
## XVector 0.30.0 2020-10-27 [1] RSPM (R 4.0.4)
## yaml 2.2.1 2020-02-01 [1] RSPM (R 4.0.3)
## yardstick * 0.0.7 2020-07-13 [1] RSPM (R 4.0.3)
## zip 2.1.1 2020-08-27 [1] RSPM (R 4.0.3)
## zlibbioc 1.36.0 2020-10-27 [1] RSPM (R 4.0.4)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library